Package org.biojava.bio.structure

Interfaces and classes for protein structure (PDB).

See:
Description

Interface Summary

AminoAcid	AminoAcid inherits most from Hetatom.
Atom	simple interface of an Atom.
Chain	Defines the interface for a Chain.
Group	This is the datastructure for a single Group of atoms.
Structure	Interface for a structure object.

Class Summary

AlphaCTools	AlphaCTools is a collection of static convenience methods for dealing with Alpha Carbon Backbone Phi / Psi angles.
AminoAcidImpl	AminoAcid inherits most from Hetatom.
AtomImpl	Implementation of an Atom of a PDB file.
AtomIterator	an iterator over all atoms of a structure / group.
Calc	utility operations on Atoms, AminoAcids, etc.
ChainImpl	A Chain in a PDB file.
GroupIterator	an iterator over all groups of a structure.
HetatomImpl	Generic Implementation of a Group interface.
Mutator	A class that can change one amino acid to another.
NucleotideImpl	A nucleotide group is almost the same as a Hetatm group.
StandardAminoAcid	A class that provides a set of standard amino acids
StructureImpl	Implementation of a PDB Structure.
StructureTools	a class that provides some tool methods
SVDSuperimposer	a class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...

Exception Summary

StructureException

An exception during the parsing of a PDB file.

Package org.biojava.bio.structure Description

Interfaces and classes for protein structure (PDB).